1. Field of the Invention
This invention relates to the fabrication of biochip arrays. In particular, the invention relates to the characterization, optimization, and quality control of bioarrays fabricated from porous media. More particularly, the invention relates to a method for determining the size, size distribution, and spatial distribution of the pores of a porous substrate, and even more particularly, the invention relates to a method for determining the size, size distribution, and spatial distribution of the pores of a polymeric hydrogel-based substrate.
2. Background of the Invention
Microfabricated arrays (biochips) of oligonucleotides, nucleic acids, or peptides have utility in a wide variety of applications, including DNA and RNA sequence analysis, diagnostics of genetic diseases, gene polymorphism studies, analysis of gene expression, and studies of receptor-ligand interactions. In the process of biochip fabrication, large numbers of probe molecules are bound to small, defined regions of a substrate. Glass slides, silicon wafers, or polymeric hydrogels may be used as a biochip substrate, with a two-dimensional or three-dimensional substrate surface utilized for probe attachment. As compared to two-dimensional biochip substrates, three-dimensional substrates offer an advantage of increased sensitivity. This increased sensitivity results from the larger surface area of three-dimensional substrates, allowing for the immobilization of a greater number of probe molecules in a fixed two-dimensional area, and in turn permitting the interaction of a greater number of bound probe molecules with target molecules (biomolecules) in a given sample.
Polymeric hydrogels offer several advantages over both glass and silicon as a substrate material for biochip preparation. One of the primary advantages for using porous hydrogel media over other substrate materials is that the polymeric hydrogel matrix is inherently a three-dimensional porous structure, which eliminates the need to perform lithography and etching to form artificial three-dimensional structures. Yet, while the inherent three-dimensional structure of porous hydrogel media can be advantageous, this structure also creates potential difficulties when porous hydrogel material is used as a substrate in the manufacture of biochip arrays.
The optimization and characterization of substrate structure during the preparation of porous hydrogel media, for example, can be particularly problematic. The size, size distribution, and spatial distribution of the pores in a polymeric hydrogel array are important factors in preparing a suitable three-dimensional biochip substrate. For example, if the pores of the porous hydrogel media are not large enough, reaction efficiency may be adversely affected as biomolecules in a given test sample are prevented or restricted from freely interacting with probe molecules bound to the substrate surface. In the manufacturing of porous hydrogel media, a pore size that is approximately an order of a magnitude larger than the largest biomolecules in the sample is desired. However, no methods for directly determining the characteristics of polymeric hydrogel pores are presently available. This is primarily a result of the physical properties of hydrogel porous media, i.e., that the material is soft and easily collapsible, and thus incompatible with currently-available characterization methods. For example, methods such as scanning electron microscopy (SEM), Atomic Force Microscopy (AFM), and Scanning Tunneling Microscopy (STM) cannot currently be used to characterize the structure of hydrogel porous media during the manufacturing process. Thus, there remains a need in the art for a method to characterize and optimize the structure of porous hydrogel media. Additionally, there is also a need in the art for a method to perform quality control on the structure of porous hydrogel media.
The invention provides a method for characterizing the structure of porous media, primarily for use in the fabrication of bioarrays. More particularly, the invention provides a method for determining the size, size distribution, and spatial distribution of the pores of a porous substrate, and even more particularly, the invention provides a method for determining the size, size distribution, and spatial distribution of the pores of a polymeric hydrogel-based substrate. This is achieved by depositing metal onto the porous media to produce a mechanically stable matrix, which, in turn, is capable of withstanding characterization by standard methods in the art, such as SEM, AFM, or STM.
The method of the present invention offers several advantages over the prior art. For example, the method permits for the direct characterization of the structure of porous media, more particularly the method permits the direct determination of the size, size distribution, and spatial distribution of the pores of a porous hydrogel substrate. Furthermore, the method is capable of determining the structure of porous hydrogel media in its native state, since no method-induced artifacts are introduced into the media during the process of depositing metal onto the porous media and the process can be performed on porous hydrogel media in its hydrated state.
Specific preferred embodiments of the present invention will become evident from the following more detailed description of certain preferred embodiments and the claims.